Quantification of human astroviruses in sewage using real-time RT-PCR

Leveraging machine learning for taxonomic classification of emerging astroviruses

Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens. Astrovirus taxonomic classification includes two genera, Avastrovirus and Mamastrovirus. However, with next-generation sequencing, broader interspecies transmission has been observed necessitating a reexamination of the current host-based taxonomic classification approach. In this study, a novel taxonomic classification method is presented for emergent and as yet unclassified astroviruses, based on whole genome sequence k-mer composition in addition to host information. An optional component responsible for identifying recombinant sequences was added to the method's pipeline, to counteract the impact of genetic recombination on viral classification. The proposed three-pronged classification method consists of a supervised machine learning method, an unsupervised machine learning method, and the consideration of host species. Using this three-pronged approach, we propose genus labels for 191 as yet unclassified astrovirus genomes. Genus labels are also suggested for an additional eight as yet unclassified astrovirus genomes for which incompatibility was observed with the host species, suggesting cross-species infection. Lastly, our machine learning-based approach augmented by a principal component analysis (PCA) analysis provides evidence supporting the hypothesis of the existence of human astrovirus (HAstV) subgenus of the genus Mamastrovirus, and a goose astrovirus (GoAstV) subgenus of the genus Avastrovirus. Overall, this multipronged machine learning approach provides a fast, reliable, and scalable prediction method of taxonomic labels, able to keep pace with emerging viruses and the exponential increase in the output of modern genome sequencing technologies.

Molecular characteristics and pathogenicity of a novel chicken astrovirus variant

It is well-established that the genetic diversity, regional prevalence, and broad host range of astroviruses significantly impact the poultry industry. In July 2022, a small-scale commercial broiler farm in China reported cases of growth retardation and a 3% mortality rate. From chickens displaying proventriculitis and pancreatitis, three chicken astroviruses (CAstV) isolates were obtained and named SDAU2022-1-3. Complete genomic sequencing and analysis revealed the unique characteristics of these isolates from known CAstV strains in ORF1a, ORF1b, and ORF2 genes, characterized by an unusually high variability. Analysis of amino acid mutations in ORF1a, ORF1b, and ORF2 indicated that the accumulation of these mutations played a pivotal role in the emergence of the variant strain. Inoculation experiments demonstrated that affected chickens exhibited liver and kidney enlargement, localized proventricular hemorrhage, and a dark reddish-brown appearance in about two-thirds of the pancreas. Histopathological examination unveiled hepatic lymphocytic infiltration, renal tubular epithelial cell swelling, along with lymphocytic proventriculitis and pancreatitis. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis indicated viremia and viral shedding at 3 days post-infection (dpi). The proventriculus displayed the highest viral loads, followed by the liver, kidney, duodenum, and pancreas. Liver parameters (AST and ALT) and kidney parameters (UA and UN) demonstrated mild damage consistent with earlier findings. While the possibility of new mutations in the ORF2 gene of CAstV causing proventriculitis and pancreatitis warrants further investigation, these findings deepen our comprehension of CAstV's pathogenicity in chickens. Additionally, they serve as valuable references for subsequent research endeavors.

Norovirus and sapovirus infections after allogeneic hematopoietic stem cell transplantation: is it worth it to look for them?

Norovirus (NoV) and Sapovirus (SaV) are potential causative agents of diarrhea after allogeneic HSCT but little is known in this population. We performed a retrospective analysis by RT-PCR of calicivirus (NoV and SaV), Human adenovirus (HAdV), rotavirus (RV), Aichi virus (AiV), enterovirus (EV), human parechovirus (HPeV) and Human bocavirus (HBoV) in the diarrheal stools of patients after allogeneic HSCT. 49/162 patients had positive viral assays: HAdV (17%), EV (7%), NoV (4.3%), RV and HBoV (3.1% each), SaV (1.9%), AiV (1.2%), HPeV (0.6%). Seven patients were positive for NoV and 3 for SaV. Among viruses-positive samples, the frequency of caliciviruses cases was 7% in the 6 months post-HSCT compared to 40% after (p < 0.0001). The median duration of symptom was 0.7 months but 2 cases, occurring more than one year after HSCT, were chronic, undiagnosed and strongly contributed to morbidity. Systematic testing of caliciviruses appears especially useful in late chronic diarrhea.

Predicting the concentrations of enteric viruses in urban rivers running through the city center via an artificial neural network

Viral waterborne diseases are widespread in cities due largely to the occurrence of enteric viruses in urban rivers, which pose a significant concern to human health. Yet, the application of rapid detection technology for enteric viruses in environmental water remains undeveloped globally. Here, multiple linear regression (MLR) modeling and artificial neural network (ANN) modeling, which used frequently measured physicochemical parameters in river water, were constructed to predict the concentration of enteric viruses including human enteroviruses (EnVs), rotaviruses (HRVs), astroviruses (AstVs), noroviruses GⅡ (HuNoVs GⅡ), and adenoviruses (HAdVs) in rivers. After training, testing, and validating, ANN models showed better performance than any MLR model for predicting the viral concentration in Jinhe River. All determined R-values for ANN models exceeded 0.89, suggesting a strong correlation between the predicted and measured outputs for target enteric viruses. Furthermore, ANN models provided a better congruence between the observed and predicted concentrations of each virus than MLR models did. Together, these findings strongly suggest that ANN modeling can provide more accurate and timely predictions of viral concentrations based on frequent (or routine) measurements of physicochemical parameters in river water, which would improve assessments of waterborne disease prevalence in cities.

Sources, fates and treatment strategies of typical viruses in urban sewage collection/treatment systems: A review

The ongoing coronavirus pandemic (COVID-19) throughout the world has severely threatened the global economy and public health. Due to receiving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a wide variety of sources (e.g., households, hospitals, slaughterhouses), urban sewage treatment systems are regarded as an important path for the transmission of waterborne viruses. This review presents a quantitative profile of the concentration distribution of typical viruses within wastewater collection systems and evaluates the influence of different characteristics of sewer systems on virus species and concentration. Then, the efficiencies and mechanisms of virus removal in the units of wastewater treatment plants (WWTPs) are summarized and compared, among which the inactivation efficiencies of typical viruses by typical disinfection approaches under varied operational conditions are elucidated. Subsequently, the occurrence and removal of viruses in treated effluent reuse and desalination, as well as that in sewage sludge treatment, are discussed. Potential dissemination of viruses is emphasized by occurrence via aerosolization from toilets, the collection system and WWTP aeration, which might have a vital role in the transmission and spread of viruses. Finally, the frequency and concentration of viruses in reclaimed water, the probability of infection are also reviewed for discussing the potential health risks.

Oyster Crassostrea gigas, a good model for correlating viral and chemical contamination in the marine environment

To establish a relationship between viruses and chemicals, they were analysed in oyster Crassostrea gigas from an Italian experimental station. The chemicals concentrations were: Σ6 NDL-PCBs 0.82-7.12 ng g^-1; BaP LOQ (<0.2 μg kg^-1) to 1.2 μg kg^-1; PAH4 LOQ (<0.2 μg kg^-1) to 9.8 μg kg^-1; Cd 0.073-0.365 mg kg^-1; Pb 0.010-0.487 mg kg^-1; and Hg < LOQ (0.089 mg kg^-1). The viruses identified included: noroviruses (NoVGI/GII), astrovirus (AsV), rotavirus (RV), adenovirus (AdV), and sapovirus (SaV), while hepatitis A, hepatitis E, and Aichi viruses were not detected. Significant correlations were observed for NDL-PCBs with NoVGI, NoVGII, and AdV; BaP and PAH4 with NoVGI and AsV; Cd with RV; Pb with NoVGI and AsV; PAHs with Pb; AsV with NoVGI; and AdV with NoVGII. The study indicated as C. gigas is a model for correlating pollutants and foodborne viruses, whose co-presence may represent an additional food safety risk.

Experimental Methods to Study the Pathogenesis of Human Enteric RNA Viruses

Every year, millions of children are infected with viruses that target the gastrointestinal tract, causing acute gastroenteritis and diarrheal illness. Indeed, approximately 700 million episodes of diarrhea occur in children under five annually, with RNA viruses norovirus, rotavirus, and astrovirus serving as major causative pathogens. Numerous methodological advancements in recent years, including the establishment of novel cultivation systems using enteroids as well as the development of murine and other animal models of infection, have helped provide insight into many features of viral pathogenesis. However, many aspects of enteric viral infections remain elusive, demanding further study. Here, we describe the different in vitro and in vivo tools available to explore different pathophysiological attributes of human enteric RNA viruses, highlighting their advantages and limitations depending upon the question being explored. In addition, we discuss key areas and opportunities that would benefit from further methodological progress.

Detection of multiple viruses potentially infecting humans in sewage water from Xinjiang Uygur Autonomous Region, China

The progress of sequencing technologies has facilitated metagenomics projects on environmental samples like sewage water. The present study concerned the analysis of sewage samples collected from 3 locations in Xinjiang Uygur Autonomous Region in China. The analysis focused on RNA viruses known to infect humans and identified viruses from 10 families. The proportion of human virus species in the sewage samples was relatively stable with an average of 17%. Thirty virus species known to infect humans were identified and they belonged to 6 families: Picornaviridae (12), Astroviridae (11), Reoviridae (3), Caliciviridae (2), Papillomaviridae (1) and Picobirnaviridae (1). A total of 16 full-length genomes were generated from Astroviridae, Picornaviridae (Salivirus and Kobuvirus) and Picobirnaviridae. Astroviruses appeared to be the most present viruses and were detected in all sewage samples. Analyzing the virome of sewage samples should help to monitor any potential risks to public health.

Levels of human Rotaviruses and Noroviruses GII in urban rivers running through the city mirror their infection prevalence in populations

Enteric viruses exposed to water pose a huge threat to global public health and can lead to waterborne disease outbreaks. A sudden increase in enteric viruses in some water matrices also underpins the prevalence of corresponding waterborne diseases in communities over the same time period. However, few efforts have been focused on water matrices whose viral pollution may best reflect the clinical prevalence in communities. Here, a one-year surveillance of human enteric viruses including Enteroviruses (EnVs), Rotaviruses (HRVs), Astroviruses (AstVs), Noroviruses GII (HuNoVsGII) and Mastadenoviruses (HAdVs) in four representative water matrices: an urban river (UR) running through city, effluent from Wastewater Treatment Plant (EW), raw water for Urban Water Treatment Plant (RW), and tap water (TW) were performed by qPCR. The relationship between the virus detection frequency at each site and their prevalence in clinical PCR assay was further analyzed. We found that the detection frequencies of HRVs, HuNoVsGII, and AstVs in stools peaked in winter, while EnVs peaked in autumn. No EnVs occurred in EW, RW, or TW, but HuNoVsGII and AstVs occurred intensively in winter. For UR, all types of enteric viruses could be detected and the levels of acute gastroenteritis viruses (HRVs, HuNoVsGII, AstVs, and HAdVs) were highest in autumn or winter, whereas EnVs peaked in summer. In terms of correlation analyses, only HRVs and HuNoVsGII levels in UR showed a strong positive correlation with their prevalence in clinical stool samples. This study indicated that HRVs and HuNoVsGII levels in URs may mirror the local virus prevalence, thereby implying the possibility of revealing their local epidemiology by monitoring them in the URs.

Circulation of classic and recombinant human astroviruses detected in South Africa: 2009 to 2014

BACKGROUND

Astroviruses (AstVs) are associated with diarrhoeal and extra-intestinal infections in human, animal and avian species. A prevalence of 7% was reported in selected regions in SA while AstVs detected from clinical stool specimens were almost identical phylogenetically to strains identified in environmental and water samples. This study investigated the molecular diversity of astroviruses circulating between 2009 and 2014 in South Africa (SA).

METHODS

Astroviruses detected in stool specimens collected from hospitalised children were investigated retrospectively. Astroviruses were characterised using type-specific RT-PCR, partial nucleotide sequence analyses in ORF1 and ORF2 and whole genome sequencing. Different genotypes were compared with clinical features to investigate genotype-related associations. The Vesikari severity scale (VSS) was evaluated for scoring astrovirus diarrhoeal infections.

RESULTS

Of 405 astroviruses detected, 49.9 % (202/405) were characterised into 32 genotypes comprising 66.3 % (134/202) putative-recombinants and 33.7 % (68/202) classic strains. No trends by year of collection, age or site were observed. Whole genome analysis in eight strains revealed that genotypes assigned by partial nucleotide sequence analyses to five astroviruses were incorrect. Bivariate analyses showed there were no significant associations between genotypes and clinical symptoms or severity of infection. A comparison of Vesikari parameters with astrovirus-positive proxy values demonstrated that Vesikari scores for duration of diarrhoea and admission temperatures would result in a milder infection rating in astrovirus-positive cases.

CONCLUSIONS

Diverse genotypes co-circulated with putative-recombinants predominating. Astrovirus classification was complicated by the lack of a consistent characterisation system and reliable reference database. The VSS should be used cautiously to rate astrovirus diarrhoea. While surveillance in communities and out-patient clinics must be continued, screening for human astroviruses in alternate hosts is needed to determine the reservoir species.

Contamination sources of the enteric virus in recreational marine water shift in a seasonal pattern

Human enteric virus occurrence in bathing beaches poses a potential health risk to swimmers. They may come from several sources, but the understanding of the seasonal contribution of contamination sources to virus occurrence is still lacking. Here, the surveillance of human enteric viruses at the First Bathing Beach in Qingdao was performed January-December 2018. The occurrence of Enteric viruses, assayed with quantitative polymerase chain reaction (qPCR), was analyzed at temporal and spatial levels to determine the viral contamination sources. The results showed that only Astroviruses (AstVs) and Adenoviruses (HAdVs) were found in the swimming area. Their occurrence correlated significantly with the sewage-polluted area, but HAdVs were only found in autumn and AstVs in spring. Meanwhile, enteric viruses in the swimming area showed significantly higher levels than the surrounding area, particularly AstVs in summer with the swimmer crowd. All these data imply that sewage discharge and swimmers co-contribute to the viral occurrence in a seasonal pattern, with the former being more focused in warm seasons (spring and autumn) and the latter in hot seasons (summer). These results indicate that sewage discharge and crowd swimmers, as unsafe swimming conditions, should be avoided to improve public health at the bathing beaches.

The Isolation and Molecular Characterization of an Astrovirus From "Yellow" Chickens, China

Chicken astrovirus (CAstV) infection is strongly associated with kidney disease, gout, “white chicks” hatchery disease, and runting and stunting syndrome (RSS). In the present study, 82.5% of 154 clinical samples from different provinces in China were positive for CAstV by RT-PCR. One CAstV isolate, designated as AAstV/Chicken/CHN/2017/NJ01, was successfully isolated from the small intestine of “Yellow” chickens using LMH cells. The genome sequence and structure analyses revealed that NJ1701 had the typical characteristics of avian astroviruses which was genetically distinct from other Avastrovirus. This isolate was classified as Group B subgroup i based on phylogenetic analysis of complete ORF2 (capsid) amino acid sequences. Meanwhile, growth depression and hatchability reduction were observed in the chicken embryo infection experiment. The results in the current study will contribute to our understanding of chicken astrovirus in China.

Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation

BACKGROUND

Acute gastroenteritis is an important cause of childhood morbidity and mortality worldwide. A number of pathogens are responsible for human acute gastroenteritis. The recent introduction of syndromic assays for the diagnosis of enteric infections, including a wide panel of enteric pathogens, has unveiled the frequency of mixed infections. This study was carried out to assess the burden of viral co-infections and the genetic diversity of the viruses detected in children hospitalized with acute gastroenteritis in Italy.

METHODS

A total of 4161 stool samples collected from diarrheic children over 11 years, from January 2008 to December 2018, were investigated for the presence of four enteric viruses, i.e. group A rotavirus, norovirus, astrovirus and adenovirus. The samples were initially screened by either molecular or immunochromatographic assays and subsequently confirmed by Real-time PCR and sequence analyses.

RESULTS

At least one viral agent was detected in 48.6 %of specimens. Rotavirus was the most prevalent virus (24.7 %) followed by norovirus (19.6 %), adenovirus (5.3 %) and astrovirus (3%). Co-infections were detected in 8.3 % of virus-positive patients, with common viral combination being rotavirus with norovirus (70.6 % of co-infections) or with astrovirus (9.6 %). A variety of viral genotypes was detected in co-infections and in single infections. Using Real-time PCR cycle thresholds as a proxy measure of fecal viral load, rotavirus was generally detected at higher levels in co-infected patients.

CONCLUSIONS

Combining and deciphering measurable indicators of viral load and epidemiological information could be useful for an accurate interpretation of viral co-infections.

Evaluation of the RIDA®GENE RT-PCR assays for detection of sapovirus, astrovirus, adenovirus, and rotavirus in stool samples of adults in Switzerland

Sapovirus (SaV) and astrovirus (AstV) increasingly are recognized as cause of acute viral gastroenteritis (AGE). We evaluated the real-time RT-PCR assays RIDA®GENE SaV and viral stool panel II (RGN RT-PCR) for detection of SaV, AstV, adenovirus (AdV) F40/41 and rotavirus (RoV) in clinical stool samples (n = 69). Results were compared with reference singleplex RT-PCRs. The sensitivity for SaV, AstV and RoV are 100%, the specificity ranges from 98.1% to 100%. In 10 out of 11 AdV (all types) samples, the RGN RT-PCR for AdV F40/41 displayed negative results. Retrospectively, 196 stool specimens from adult patients previously tested negative for norovirus (NoV) were analyzed. In about 10% of NoV-negative stool samples, AdV (n = 9), RoV (n = 6), AstV (n = 3) or SaV (n = 3) were found. The RGN RT-PCR assays are useful for detection of enteric viruses other than NoV. This study emphasizes the need for further testing of NoV-negative stool samples in patients with AGE.

Evaluation of the BioFire FilmArray Gastrointestinal Panel and Real-Time Polymerase Chain Reaction Assays for the Detection of Major Diarrheagenic Pathogens by a Multicenter Diarrheal Disease Surveillance Program in China

In the field of the detection of pathogens responsible for infectious diarrhea, multiplex nucleic acids detection technology has attracted attention due to its ability to simultaneously screen a wide range of pathogens, its simplicity to operate and a faster turnaround time. We conducted a three-center evaluation that compared the BioFire FilmArray gastrointestinal panel (FA GI) and real-time polymerase chain reaction (PCR) assays for the detection of pathogens from 462 clinical diarrhea specimens, and characterized the distribution of various pathogens that were analyzed. The sensitivity of FA GI was 100% for 13 pathogens and 93.8-98.3% for 4 pathogens, but low for Salmonella (60.5%) and adenovirus (88.9%). The sensitivity per pathogen of real-time PCR assays was lower than that observed with FA GI. The specificity of FA GI and real-time PCR assays per pathogen was greater than 94.5% and 99%, respectively. FA GI and real-time PCR assays detected ≥1 pathogen in 339 (73.4%) and 297 (64.3%) samples, respectively, and 324 (70.1%) samples were considered as positive according to the reference standard. Multiple pathogens were detected in 37.2% and 24.9% of samples by FA GI and real-time PCR assays, respectively. Norovirus GI/GII and Campylobacter were less associated with coinfections. The positive rates of some pathogens varied among the three regions of China. Molecular methods can help squickly identify the cause of diarrhea and provide valuable information for early diagnosis and optimal patient therapy.

Detection of Hepatitis A Virus and Other Enteric Viruses in Shellfish Collected in the Gulf of Naples, Italy

To assess the quality of shellfish harvest areas, bivalve mollusk samples from three coastal areas of the Campania region in Southwest Italy were evaluated for viruses over a three-year period (2015-2017). Screening of 289 samples from shellfish farms and other locations by qPCR and RT-qPCR identified hepatitis A virus (HAV; 8.9%), norovirus GI (NoVGI; 10.8%) and GII (NoVGII; 39.7%), rotavirus (RV; 9.0%), astrovirus (AsV; 20.8%), sapovirus (SaV; 18.8%), aichivirus-1 (AiV-1; 5.6%), and adenovirus (AdV, 5.6%). Hepatitis E virus (HEV) was never detected. Sequence analysis identified HAV as genotype IA and AdV as type 41. This study demonstrates the presence of different enteric viruses within bivalve mollusks, highlighting the limitations of the current EU classification system for shellfish growing waters.

Astrovirus evolution and emergence

Astroviruses are small, non-enveloped, positive-sense, single-stranded RNA viruses that belong to the Astroviridae family. Astroviruses infect diverse hosts and are typically associated with gastrointestinal illness; although disease can range from asymptomatic to encephalitis depending on the host and viral genotype. Astroviruses have high genetic variability due to an error prone polymerase and frequent recombination events between strains. Once thought to be species specific, recent evidence suggests astroviruses can spread between different host species, although the frequency with which this occurs and the restrictions that regulate the process are unknown. Recombination events can lead to drastic evolutionary changes and contribute to cross-species transmission events. This work reviews the current state of research on astrovirus evolution and emergence, especially as it relates to cross-species transmission and recombination of astroviruses.

Wastewater-Based Epidemiology for Early Detection of Viral Outbreaks

The immense global burden of infectious disease outbreaks and the need to establish prediction and prevention systems have been recognized by the World Health Organization (WHO), the National Institutes of Health (NIH), the United States Agency of International Development (USAID), the Bill and Melinda Gates Foundation, and the international scientific community. Despite multiple efforts, this infectious burden is still increasing. For example, it has been reported that between 1.5 and 12 million people die each year from waterborne diseases and diarrheal diseases are listed within the top 15 leading causes of death worldwide. Rapid population growth, climate change, natural disasters, immigration, globalization, and the corresponding sanitation and waste management challenges are expected to intensify the problem in the years to come.

Occurrence of microbial indicators, pathogenic bacteria and viruses in tropical surface waters subject to contrasting land use

Fecal indicator bacteria, such as Escherichia coli (E.coli) and Enterococcus, have been widely used to indicate the presence of pathogens. However, the suitability of fecal indicator bacteria to represent health risks is still being challenged, particularly in tropical aquatic environments. The objective of this study is to understand the occurrence and prevalence of indicators and pathogens in areas with contrasting land use, as well as to identify the major correlations between indicators, pathogens and environmental parameters. The spatial and temporal variation of indicators and pathogens was studied to examine the distribution patterns for areas with different land use, and the impact of seasonal changes on microbial populations. A total of 234 water samples were sampled for two years from reservoirs and their tributaries, and tested for fecal indicator bacteria, coliphages, human specific markers, pathogenic bacteria and viruses. The prevalence of indicators and pathogens in reservoirs were generally low, while relatively high concentrations were observed in tributaries to varying degrees. Of the enteric viruses, norovirus GII was among the most prevalent and had the highest concentration. Although strong correlations were found between indicators, only relatively weak correlations were found between indicators and pathogens. The results in this study showed that none of the bacteria/phage indicators were universal predictors for pathogens. Inclusion of the alternative indicators, Methanobrevibacter smithii, Bacteroides and human polyomaviruses (HPyVs) to monitoring programs could help to determine whether the fecal source was human. The microbial distribution patterns allow the classification of sampling sites to different clusters and thus, help to identify sites which have poor water quality. This approach will be useful for water quality management to pinpoint factors that influence water quality and help to prioritize sites for restoration of water quality.

Detection of Human Enteric Viruses in French Polynesian Wastewaters, Environmental Waters and Giant Clams

Lack of wastewater treatment efficiency causes receiving seawaters and bivalve molluscan shellfish to become contaminated, which can lead to public health issues. Six wastewater samples, five seawater samples and three batches of giant clams from Tahiti (French Polynesia) were investigated for the presence of enteric viruses, but also if present, for the diversity, infectivity and integrity of human adenoviruses (HAdV). Enteroviruses (EV), sapoviruses (SaV) and human polyomaviruses (HPyV) were detected in all wastewater samples. In decreasing frequency, noroviruses (NoV) GII and HAdV, rotaviruses (RoV), astroviruses (AsV), NoV GI and finally hepatitis E viruses (HEV) were also observed. Nine types of infectious HAdV were identified. HPyV and EV were found in 80% of seawater samples, NoV GII in 60%, HAdV and SaV in 40% and AsV and RoV in 20%. NoV GI and HEV were not detected in seawater. Intact and infectious HAdV-41 were detected in one of the two seawater samples that gave a positive qPCR result. Hepatitis A viruses were never detected in any water types. Analysis of transcriptomic data from giant clams revealed homologues of fucosyltransferases (FUT genes) involved in ligand biosynthesis that strongly bind to certain NoV strains, supporting the giant clams ability to bioaccumulate NoV. This was confirmed by the presence of NoV GII in one of the three batches of giant clams placed in a contaminated marine area. Overall, all sample types were positive for at least one type of virus, some of which were infectious and therefore likely to cause public health concerns.

A relationship between environmental pollutants and enteric viruses in mussels(Mytilus galloprovincialis)

Mussels can be affected by environmental contaminants, as non-dioxin-like polychlorinated biphenyls (NDL-PCBs), polycyclic aromatic hydrocarbons (PAHs) and cadmium (Cd). Moreover, mussels may concentrate human enteric viruses, like noroviruses (NoVGI/GII), astrovirus (AsV) and rotavirus (RV). Herein, to establish a relationship between environmental and viral contamination, with the aim to ensure human food safety, both chemical and microbiological analysis were carried out in mussels Mytilus galloprovincialis, farmed in Campania region (Italy). Chemical analysis revealed ranges below the European maximum limits, and were: ∑6 NDL-PCBs (28, 52, 101, 138, 153, 180) 0.579-16.857 ng g^-1 wet weight (ww); BaP LOQ (<0.2 µg kg^-1)- 2.9 µg kg^-1 ww, and ∑4 PAHs (BaA, CHR, BbFA, BaP) 0.7-23.7 µg kg^-1 ww; Cd LOQ (<0.005 mg kg^-1)- 0.078 mg kg^-1 ww. In addition, mussels exhibited a prevalence of NoVGI (18%), NoVGII (43%), AsV (40%), RV (30%) and the presence of more than one viruses resulted in about 35%. Overall, a simultaneous contamination, both chemical and viral, was found in 62% of samples. Interestingly, virus-positive mussels showed levels of chemicals higher than negative ones.

Vomiting symptom of acute gastroenteritis estimated from epidemiological data can help predict river contamination by human pathogenic enteric viruses

Contamination of fresh water bodies by human enteric viruses from wastewater discharge is a well-established phenomenon. Here we propose a model of viral contamination of rivers based on acute gastroenteritis epidemiology and assess how well it can simulate in situ experimental monitoring. Noroviruses, rotaviruses, enteroviruses, adenoviruses and hepatitis A viruses were quantified by molecular methods after water concentration. Water flows were obtained from the Hydro databank and wastewater treatment plant (WWTP) data. Acute gastroenteritis cases based on medical prescriptions were recorded by the French public health agency. We estimated the total number of daily viral acute gastroenteritis cases and modeled virus shedding and fate in WWTPs and rivers. Simulated virus concentrations were compared to the weighted sum of measured concentrations. Seasonal variations in viral acute gastroenteritis were predicted from vomiting occurrence. All viruses except hepatitis A virus were widely detected in wastewaters and river, in concentrations reaching 10⁺⁶ genome copies·L^-1 for adenoviruses in the Artière River. We were able to predict virus load in raw wastewater and in the Artière River. Estimated weighting coefficients showed the high impact of noroviruses GII. This model can thus serve to compare water treatment, discharge and reuse scenarios.

Total coliforms as an indicator of human enterovirus presence in surface water across Tianjin city, China

BACKGROUND

Enteric viruses in surface water pose considerable risk to morbidity in populations living around water catchments and promote outbreaks of waterborne diseases. However, due to poor understanding of the correlation between water quality and the presence of human enteric viruses, the failure to assess viral contamination through alternative viral indicators makes it difficult to control disease transmission.

METHODS

We investigated the occurrence of Enteroviruses (EnVs), Rotaviruses (HRVs), Astroviruses (AstVs), Noroviruses GII (HuNoVs GII) and Adenoviruses (HAdVs) from Jinhe River over 4 years and analyzed their correlation with physicochemical and bacterial parameters in water samples.

RESULTS

The findings showed that all target viruses were detected in water at frequencies of 91.7% for HAdVs, 81.3% for HuNoVs GII, 79.2% for EnVs and AstVs, and 70.8% for HRVs. These viruses had a seasonal pattern, which showed that EnVs were abundant in summer but rare in winter, while HAdVs, HRVs, AstVs, and HuNoVs GII exhibited opposite seasonal trends. Pearson correlation analysis showed that total coliforms (TC) was significantly positively correlated with EnVs concentrations while no consistent significant correlations were observed between bacterial indices and viruses that precipitate acute gastroenteritis.

CONCLUSIONS

Taken together, the findings provide insights into alternative viral indicators, suggesting that TC is a potentially promising candidate for assessment of EnVs contamination. However, it failed to predict the presence of HAdVs, HRVs, AstVs, and HuNoVs GΙΙ in surface water across the city of Tianjin.

Epidemiology of human astroviruses among children younger than 5 years: Prospective hospital-based sentinel surveillance in South Africa, 2009-2014

BACKGROUND

The epidemiology of human astroviruses (HAstVs) in hospitalised patients less than 5 years of age from selected sites in South Africa was investigated. Diarrheagenic stool specimens collected from April 2009 to May 2014 were screened retrospectively for selected viruses, bacteria and parasites.

METHOD

Patient data were analysed to identify epidemiologic factors most frequently detected with HAstV infections. The following case-comparisons were investigated; HAstV-positive and HAstV-negative children, human immunodeficiency virus (HIV)-infected and HIV-uninfected (HAstV-positive) children and HIV-exposed and unexposed (HAstV-positive HIV-uninfected) children.

RESULTS

Astrovirus was identified in 7.0% (234/3340) of cases and most frequently in ages 7 to 12 months (9.2%; 90/975) compared with 5.8% to 6.6% in other 6-month age groups. No seasonal trends were observed. More HAstVs were detected in children from homes that used outdoor water sources (7.6%) compared to indoor sources [5.7%; adjusted odds ratio (aOR), 1.5; 95% CI, 1.1-2.1; P = 0.009]. Astroviruses were detected in 8.4% (67/799) of HIV-uninfected patients that were exposed to HIV compared with 5.9% (74/1257) of HIV-unexposed patients ( P = 0.032).

CONCLUSION

Astroviruses were most prevalent in children aged 7 to 12 months and were detected throughout the study period. The study was limited as only hospitalised patients were investigated and no comparisons were made to diarrhoea-free control groups. Future HAstV surveillance should include community-based studies and children presenting at outpatient facilities.

Preliminary evaluation of BioFire FilmArray® Gastrointestinal Panel for the detection of noroviruses and other enteric viruses from wastewater and shellfish

The BioFire FilmArray^® Gastrointestinal Panel was evaluated for the rapid detection of adenovirus, astrovirus, norovirus, rotavirus and sapovirus from influent and effluent wastewater and shellfish. The multiplex BioFire FilmArray^® Gastrointestinal Panel compared well to singleplex qPCR/RT-qPCR methods for the detection of adenovirus, astrovirus, rotavirus and sapovirus from influent and effluent wastewater samples. However, the BioFire FilmArray^® Gastrointestinal Panel showed poor performance for the detection of norovirus, significantly underestimating its presence in wastewater and shellfish samples when compared with the singleplex norovirus GI and GII RT-qPCR assays. Therefore, improvement on detection efficiency for norovirus from environmental and food samples is necessary before using results from the FilmArray^® Gastrointestinal Panel to assess associated public health risks.

Molecular Detection of Human Astrovirus in Children With Gastroenteritis, Northern Italy

BACKGROUND

Human astroviruses have increasingly been identified and are important agents of diarrheal disease, especially in infants and young children. This article presents the real-time polymerase chain reaction TaqMan assay for the detection and quantification of human astrovirus for clinical fecal samples collected from hospitalized children with acute gastroenteritis in Piedmont (northern Italy) from December 2014 to November 2015.

METHODS

A total of 159 fecal specimens from hospitalized children with acute gastroenteritis, previously screened for rotavirus, adenovirus, norovirus, human parechovirus, salivirus and sapovirus, were tested for human astrovirus.

RESULTS

The most commonly detected virus was norovirus GII (33.8%), followed by rotavirus (21.3%), sapovirus (10.9%), human parechovirus (8%), norovirus GI (6.7%), adenovirus (1%) and salivirus (0.52%). A total of 30 of 159 (18.87%) episodes of acute gastroenteritis were associated with human astrovirus genomic detection.

CONCLUSIONS

Our data showed that the detection rate of astrovirus in diarrheal children (18.87%) was higher than observed in other countries, where they were reported in diarrheal children in 10.3%-0.8% of patients and a mean incidence worldwide of 11%. Our data showed that the detection rate of astrovirus in pediatric gastroenteritis was greater than previously reported in Italy.

Waterborne outbreak of gastroenteritis on the KwaZulu-Natal Coast, South Africa, December 2016/January 2017

An unexpected increase in gastroenteritis cases was reported by healthcare workers on the KwaZulu-Natal Coast, South Africa, January 2017 with >600 cases seen over a 3-week period. A case-control study was conducted to identify the source and risk factors associated with the outbreak so as to recommend control and prevention measures. Record review identified cases and controls and structured-telephonic interviews were conducted to obtain exposure history. Stool specimens were collected from 20 cases along with environmental samples and both screened for enteric pathogens. A total of 126 cases and 62 controls were included in the analysis. The odds of developing gastroenteritis were 6.0 times greater among holiday makers than residents (95% confidence interval (CI) 2.0-17.7). Swimming in the lagoon increased the odds of developing gastroenteritis by 3.3 times (95% CI 1.06-10.38). Lagoon water samples tested positive for norovirus (NoV) GI.6, GII.3 and GII.6, astrovirus and rotavirus. Eleven (55%) stool specimens were positive for NoV with eight genotyped as GI.1 (n = 2), GI.5 (n = 3), GI.6 (n = 2), and GI.7 (n = 1). A reported sewage contamination event impacting the lagoon was the likely source with person-to-person spread perpetuating the outbreak. Restriction to swimming in the lagoon was apparently ineffective at preventing the outbreak, possibly due to inadequate enforcement, communication and signage strategies.

Detection and quantification of soil-transmitted helminths in environmental samples: A review of current state-of-the-art and future perspectives

It is estimated that over a billion people are infected with soil-transmitted helminths (STHs) globally with majority occurring in tropical and subtropical regions of the world. The roundworm (Ascaris lumbricoides), whipworm (Trichuris trichiura), and hookworms (Ancylostoma duodenale and Necator americanus) are the main species infecting people. These infections are mostly gained through exposure to faecally contaminated water, soil or contaminated food and with an increase in the risk of infections due to wastewater and sludge reuse in agriculture. Different methods have been developed for the detection and quantification of STHs eggs in environmental samples. However, there is a lack of a universally accepted technique which creates a challenge for comparative assessments of helminths egg concentrations both in different samples matrices as well as between locations. This review presents a comparison of reported methodologies for the detection of STHs eggs, an assessment of the relative performance of available detection methods and a discussion of new emerging techniques that could be applied for detection and quantification. It is based on a literature search using PubMed and Science Direct considering all geographical locations. Original research articles were selected based on their methodology and results sections. Methods reported in these articles were grouped into conventional, molecular and emerging techniques, the main steps in each method were then compared and discussed. The inclusion of a dissociation step aimed at detaching helminth eggs from particulate matter was found to improve the recovery of eggs. Additionally the selection and application of flotation solutions that take into account the relative densities of the eggs of different species of STHs also results in higher egg recovery. Generally the use of conventional methods was shown to be laborious and time consuming and prone to human error. The alternate use of nucleic acid-based techniques has improved the sensitivity of detection and made species specific identification possible. However, these nucleic acid based methods are expensive and less suitable in regions with limited resources and skill. The loop mediated isothermal amplification method shows promise for application in these settings due to its simplicity and use of basic equipment. In addition, the development of imaging soft-ware for the detection and quantification of STHs shows promise to further reduce human error associated with the analysis of environmental samples. It may be concluded that there is a need to comparatively assess the performance of different methods to determine their applicability in different settings as well as for use with different sample matrices (wastewater, sludge, compost, soil, vegetables etc.).

The development of a multiplex real-time RT-PCR for the detection of adenovirus, astrovirus, rotavirus and sapovirus from stool samples

Viral gastroenteritis is a major health problem with significant morbidity and economic consequences. Viral gastroenteritis is caused by a number of viruses, including norovirus, rotavirus, adenovirus, astrovirus, and sapovirus. Conventional diagnosis is based on direct antigen detection and electron microscopy, however enzyme immunoassay's are insensitive and not available for all relevant pathogens, and electron microscope (EM) is no longer routinely carried out in most laboratories. Most laboratories now offer norovirus real-time PCR testing however the availability of other assays is variable. Commercial methods for the detection of inflectional intestinal disease (IID) are available but these can be expensive and are not commonly used. This paper describes the development of a single multiplex assay for the simultaneous detection of adenovirus, astrovirus, rotavirus and sapovirus from stool samples. The multiplex was evaluated by assessing endpoint sensitivity, specificity, panel of clinical samples, quality control (QC) panel and the robustness and reproducibility of the multiplex.

Preparation of MS2-based nanoparticles as control and standard materials for the molecular detection of dengue virus serotypes

To quantify dengue virus (DENV) and evaluate the performance of clinical laboratories using quantitative real-time polymerase chain reaction (qRT-PCR) assays, we constructed high-efficiency expression systems to produce DENV-1 to 4 nanoparticles and assessed their suitability as standard and control materials in 20 laboratories across China. Targeted gene sequences of DENV-1 to 4 were synthesized and inserted into pACYC-Duet 1-MS2 recombinant plasmids to generate corresponding nanoparticle expression systems. After collection, verification, and quantification by digital PCR (dPCR), DENV-1 to 4 nanoparticles were prepared as control and standard materials. Five positive and three negative samples of each DENV serotype in every panel were used for assessing the performance of the participating laboratories across China, as well as standard materials for the quantitative detection of DENV using qRT-PCR assays. The accuracy, sensitivity, and specificity of qRT-PCR used by the 20 evaluated laboratories were 89.6 (569/635), 85.1 (336/395), and 97.1% (233/240), respectively. Overall, sixteen (80.0%) laboratories were qualified in detecting DENV, among which five (25.0%) were designated as "competent", eleven (55.0%) were defined as "acceptable", and four (20%) were considered to be "improvable". The results generated from the DENV standard samples were significantly positively correlated with those generated by dPCR (r²=0.8698, P<0.001). In summary, DENV nanoparticles could potentially be used as controls for improving the performance of laboratories and as standards for the quantitative detection of DENV.

Epidemiology of Classic and Novel Human Astrovirus: Gastroenteritis and Beyond

Since they were identified in 1975, human astroviruses have been considered one of the most important agents of viral acute gastroenteritis in children. However, highly divergent astroviruses infecting humans have been recently discovered and associated with extra-intestinal infections. The report of cases of fatal meningitis and encephalitis, especially in immunocompromised individuals, has broadened their disease spectrum. Although zoonotic transmission among animal and human astroviruses has not been clearly recognized, the genetic similarity between some human and animal viruses makes it likely to occur. This review provides an update on the epidemiology of both classic and novel human astroviruses, and a comprehensive view on confirmed or potential association between astrovirus and human disease.

Astrovirus Diagnostics

Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.

Decay kinetics of microbial source tracking (MST) markers and human adenovirus under the effects of sunlight and salinity

Artificial seawater and freshwater microcosms inoculated with raw sewage were set up to compare the persistence of microbial source tracking (MST) markers (i.e. Bacteroides thetaiotaomicron (B. theta), Methanobrevibacter smithii (M. smithii), human polyomaviruses JC and BK (HPyVs)) and human adenoviruses under different sunlight intensity and salinity. PMA pretreatment successfully eliminated the false-positive detection of dead bacterial cells in the model-development experiment. The results were then validated using real environmental matrices in microcosms inoculated with raw sewage. The genome concentrations of the targets followed a first-order decay pattern with 90% reduction of the initial amounts in <5days for both artificial and natural surface waters. Decay rate constant (k₁) were developed microorganisms in artificial water matrices. Due to the different water environment conditions, improved decay rates (k₂) incorporated with sunlight, TSS and TOC adjustment coefficients were used for validation of the natural water matrices. Based on the predictive squared correlation coefficient (Q²_F) and root-mean-square error (RMSE) validation criteria, the improved k₂ were able to provide better prediction on the survival of target microorganisms in environmental surface waters (Q²_F>0.6 and RMSE ranged from 0.05 to 1.81). For microbial source tracking purposes, HPyVs are suggested to be better MST markers in freshwater, while B. theta is recommended for seawater based on the decay models developed in this study. The targeted DNA of M. smithii should only be used to indicate recent human faecal pollution in surface waters due to their faster decay than human adenoviruses.

Cosavirus, Salivirus and Bufavirus in Diarrheal Tunisian Infants

Three newly discovered viruses have been recently described in diarrheal patients: Cosavirus (CosV) and Salivirus (SalV), two picornaviruses, and Bufavirus (BuV), a parvovirus. The detection rate and the role of these viruses remain to be established in acute gastroenteritis (AGE) in diarrheal Tunisian infants. From October 2010 through March 2012, stool samples were collected from 203 children <5 years-old suffering from AGE and attending the Children's Hospital in Monastir, Tunisia. All samples were screened for CosV, SalV and BuV as well as for norovirus (NoV) and group A rotavirus (RVA) by molecular biology. Positive samples for the three screened viruses were also tested for astrovirus, sapovirus, adenovirus, and Aichi virus, then genotyped when technically feasible. During the study period, 11 (5.4%) samples were positive for one of the three investigated viruses: 2 (1.0%) CosV-A10, 7 (3.5%) SalV-A1 and 2 (1.0%) BuV-1, whereas 71 (35.0%) children were infected with NoV and 50 (24.6%) with RVA. No mixed infections involving the three viruses were found, but multiple infections with up to 4 classic enteric viruses were found in all cases. Although these viruses are suspected to be responsible for AGE in children, our data showed that this association was uncertain since all infected children also presented infections with several enteric viruses, suggesting here potential water-borne transmission. Therefore, further studies with large cohorts of healthy and diarrheal children will be needed to evaluate their clinical role in AGE.

Prevalence and Genetic Diversity of Enteric Viruses in Children with Diarrhea in Ouagadougou, Burkina Faso

Enteric viruses are a major cause of diarrhea in children, especially those under five years old. Identifying the viral agents is critical to the development of effective preventive measures. This study aimed to determine the prevalence and genetic diversity of common enteric viruses in children under five years old in Burkina Faso. Stool samples from children with (n = 263) and without (n = 50) diarrhea disorders were collected in Ouagadougou, Burkina Faso from November 2011 to September 2012. Rotavirus, norovirus, sapovirus, astrovirus, adenovirus and Aichivirus A were detected using real-time or end-point (RT-)PCR. Rotavirus strains were G and P genotyped by multiplex RT-PCR and other viral strains were characterized by sequencing of viral subgenomic segements. At least one viral agent was detected in 85.6% and 72% of the symptomatic and asymptomatic patients, respectively. Rotavirus (63.5%), adenovirus (31.2%) and genogroup II norovirus (18.2%) were the most prevalent viruses in symptomatic patients, but only rotavirus and genogroup II norovirus were significantly associated with diarrhea (OR: 7.9, 95%CI: 3.7-17; OR: 3.5, 95%CI: 1-11.7, respectively). Sapovirus (10.3%), astrovirus (4.9%), genogroup I norovirus (2.7%) and Aichivirus A (0.8%) were less prevalent. The predominant genotype of rotavirus was G9P[8] (36.5%), and the predominant norovirus strain was GII.4 variant 2012 (71.4%). Among sapovirus, the genogroup II (87.5%) predominated. Astrovirus type 1 (41.7%) was the most frequent astrovirus identified. Aichivirus A belonged to the three genotypes (A, B and C). Enteric adenoviruses type 40 and 41 were identified in 10.2% and 5.1% respectively. Several cases of co-infections were detected. The results highlight the high prevalence and the high diversity of enteric viruses in Burkinabe children.

A 1-Year Study on the Detection of Human Enteric Viruses in New Caledonia

Human enteric viruses occur in high concentrations in wastewater and can contaminate receiving environmental waters. Due to the lack of data on the prevalence of enteric viruses in New Caledonia, the presence and the concentrations of enteric viruses in wastewater and seawater were determined. Untreated wastewater and seawater samples were collected monthly for 1 year from a wastewater treatment plant (WWTP) and from the WWTP's outlet, located directly on a popular recreational beach. Samples were tested for norovirus genogroups I and II (NoV GI and GII), astroviruses (AsV), sapoviruses (SaV), enteroviruses (EV), hepatitis A viruses (HAV), rotaviruses (RoV), human adenoviruses (HAdV) and human polyomaviruses (HPyV). To support these data, faecal samples from cases of gastroenteritis were tested for the first time for NoV and detected in the population. NoV GI, NoV GII, EV, SaV, HAdV and HPyV were detected in all wastewaters, RoV in 75% and AsV in 67%. HAV were not detected in wastewater. Overall, 92% of seawater samples were positive for at least one virus. HPyV were detected most frequently in 92% of samples and at concentrations up to 7.7 × 10(3) genome copies/L. NoV GI, NoV GII, EV, SaV, RoV and HAdV were found in 33, 66, 41, 33, 16 and 66% of seawater samples, respectively. AsV were not detected in seawater. This study reports for the first time the presence of NoV and other enteric viruses in New Caledonia and highlights the year-round presence of enteric viruses in the seawater of a popular beach.

Elimination of viruses from domestic wastewater: requirements and technologies

Domestic wastewater contains various pathogens, which, if not sufficiently eliminated, may enter the receiving water bodies and cause water-transmitted diseases. Among the waterborne pathogens, viruses may occur, survive and/or decay much differently from bacteria in water. In many cases, the diseases caused by viruses are more severe. Therefore, research efforts are mainly directed at the behavior of viruses in water environments, as well as the elimination of viruses from wastewater. In this paper, an overview of the occurrence of viruses in wastewater is presented, together with their categories, methods of detection and potential to cause waterborne diseases. As wastewater treatment plants are critical nodes for the influx and termination of virus transmission, the behavior of viruses at each stage of treatment is reviewed. Particular attention is paid to the unit operations, which play crucial roles in virus removals, such as coagulation and membrane filtration, and that for virus inactivation, such as chemical disinfection and UV irradiation. Future needs for the development of new technologies for virus elimination, source control, and finding more suitable indicators of viral pathogens are also highlighted.

First report of an astrovirus type 5 gastroenteritis outbreak in a residential elderly care home identified by sequencing

BACKGROUND

This is the report of an outbreak of human astrovirus type 5 gastroenteritis that occurred in a residential care home for older people in June 2013 in Tayside, Scotland, and which involved seven staff members and thirteen residents. This type of astrovirus has not been found in Scotland before and is rarely described in the literature.

OBJECTIVES

Using molecular methods such as PCR and sequencing to detect the cause of this gastroenteritis outbreak and to contain the outbreak using Public Health measures.

STUDY DESIGN

Following an epidemiological investigation, stool samples were sent for routine virology and microbiology testing at the local microbiology and virology laboratory and were found to be negative. Further testing with real-time PCR and gene sequencing at the West of Scotland Specialist Virology Centre was performed. Data on the epidemiology and the response to the outbreak was collected.

RESULTS

All samples had a 99% match to human astrovirus type 5. The use of standard infection control precautions with the addition of transmission-based precautions most likely contained the spread of the virus in this situation.

CONCLUSIONS

This report illustrates the importance of using PCR and sequencing to identify pathogens such as astrovirus in outbreaks of vomiting and diarrhoea in older people particularly if routine virology and microbiology tests are negative.

Deciphering the Diversities of Astroviruses and Noroviruses in Wastewater Treatment Plant Effluents by a High-Throughput Sequencing Method

Although clinical epidemiology lists human enteric viruses to be among the primary causes of acute gastroenteritis in the human population, their circulation in the environment remains poorly investigated. These viruses are excreted by the human population into sewers and may be released into rivers through the effluents of wastewater treatment plants (WWTPs). In order to evaluate the viral diversity and loads in WWTP effluents of the Paris, France, urban area, which includes about 9 million inhabitants (approximately 15% of the French population), the seasonal occurrence of astroviruses and noroviruses in 100 WWTP effluent samples was investigated over 1 year. The coupling of these measurements with a high-throughput sequencing approach allowed the specific estimation of the diversity of human astroviruses (human astrovirus genotype 1 [HAstV-1], HAstV-2, HAstV-5, and HAstV-6), 7 genotypes of noroviruses (NoVs) of genogroup I (NoV GI.1 to NoV GI.6 and NoV GI.8), and 16 genotypes of NoVs of genogroup II (NoV GII.1 to NoV GII.7, NoV GII.9, NoV GII.12 to NoV GII.17, NoV GII.20, and NoV GII.21) in effluent samples. Comparison of the viral diversity in WWTP effluents to the viral diversity found by analysis of clinical data obtained throughout France underlined the consistency between the identified genotypes. However, some genotypes were locally present in effluents and were not found in the analysis of the clinical data. These findings could highlight an underestimation of the diversity of enteric viruses circulating in the human population. Consequently, analysis of WWTP effluents could allow the exploration of viral diversity not only in environmental waters but also in a human population linked to a sewerage network in order to better comprehend viral epidemiology and to forecast seasonal outbreaks.

Evaluation of FRNA coliphages as indicators of human enteric viruses in a tropical urban freshwater catchment

This study aimed to evaluate the relationship between FRNA coliphages (FRNA GI to GIV) and human enteric viruses (human adenoviruses, HAdV, astroviruses, AstV, noroviruses, NoV, and rotaviruses, RoV) in a tropical urban freshwater catchment. Positive associations between human-specific coliphages and human viral pathogens substantiate their use as viral indicators and in microbial source tracking. Reverse transcription qPCR was used to measure the concentrations of viruses and FRNA coliphages in concentrated water samples. Environmental water samples were also analyzed for male-specific (F+) and somatic (Som) coliphages using plaque assay. The most abundant enteric virus was NoV (55%) followed by HAdV (33%), RoV (33%), and AstV (23%), while the most abundant FRNA genogroup was GI (85%) followed by GII (48%), GIV (8%) and GIII (7%). Concentrations of human-specific coliphages FRNA GII were positively correlated with NoV, HAdV, RoV, AstV, F+ and Som (τ = 0.5 to 0.3, P < 0.05) while concentrations of animal-specific coliphages FRNA GI were negatively correlated with HAdV and RoV (τ = -0.2, P < 0.05). This study demonstrates statistical relationships between human-specific coliphages and a suite of human enteric viruses in the environment.

Waterborne pathogens: detection methods and challenges

Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.

Wastewater Analysis Indicates that Genetically Diverse Astroviruses, Including Strains Belonging to Novel Clades MLB and VA, Are Circulating within Japanese Populations

Human astroviruses (HAstVs) are a common etiological agent of infantile gastroenteritis. Recent studies revealed that novel astrovirus (AstV) strains of the MLB clade (MLB-AstVs) and VA clade (VA-AstVs), which are genetically distinct from the classic HAstVs, are circulating in the human population. In the present study, we quantified classic HAstVs as well as carried out a genetic analysis of classic and novel HAstVs in wastewater in Japan. The concentration of classic HAstVs in the influent water samples ranged from 10(4) to 10(5) copies per liter, and the amount removed by wastewater treatment was determined to be 2.4 ± 0.3 log10. Four types of classic HAstV strains (HAstV types 1, 2, 5, and 4/8) as well as novel AstV strains belonging to the MLB-2, VA-1, and VA-2 clades were identified using reverse transcription-PCR (RT-PCR) assays, including assays newly developed for the detection of strains of the MLB and VA clades, followed by cloning and nucleotide sequencing. Our results suggest that genetically diverse AstV strains are circulating among the human population in Japan. The newly developed (semi)nested RT-PCR assays for these novel AstV clades are useful to identify and characterize the novel AstVs in environmental waters.

Environmental Assessment of Classical Human Astrovirus in Uruguay

The aim of this study was to determine the molecular epidemiology of classical human astrovirus (HAstV) strains in sewage samples from four Uruguayan cities: Bella Unión, Salto, Paysandú, and Fray Bentos, located in the Northwestern region of the country. Overall, 96 sewage samples were collected biweekly between March 2011 and February 2012 and were subject to ultracentrifugation methodology in order to concentrate the viruses. RT-PCR directed to the ORF2 genome region was performed followed by sequencing and phylogenetic analysis. Forty-three (45 %) out of 96 analyzed samples were positive for HAstV (Mamastrovirus 1) and 31 of them were successfully sequenced being 21 (49 %) of them classified as HAstV-1 genotype (1a lineage) and 10 (23 %) as HAstV-2 genotype (eight strains belonging to the 2d lineage and two strains to the 2c lineage). The 1a lineage circulated throughout the year, while the 2d lineage only in the coldest months (June to October). Strikingly, the 2c lineage was detected only in Salto city during March 2011. In this city it was observed the highest frequency of HAstV and the greatest genetic diversity, probably due to its role as high touristic spot with an important influx of visitants from others regions of Uruguay and also from other countries. This study constitutes the first report in Uruguay that describes the phylogenetic diversity and genotype distribution of HAstV strains circulating in the Northwestern region evidencing a high frequency and also the presence of several different lineages.

Alternative fecal indicators and their empirical relationships with enteric viruses, Salmonella enterica, and Pseudomonas aeruginosa in surface waters of a tropical urban catchment

The suitability of traditional microbial indicators (i.e., Escherichia coli and enterococci) has been challenged due to the lack of correlation with pathogens and evidence of possible regrowth in the natural environment. In this study, the relationships between alternative microbial indicators of potential human fecal contamination (Bacteroides thetaiotaomicron, Methanobrevibacter smithii, human polyomaviruses [HPyVs], and F+ and somatic coliphages) and pathogens (Salmonella spp., Pseudomonas aeruginosa, rotavirus, astrovirus, norovirus GI, norovirus GII, and adenovirus) were compared with those of traditional microbial indicators, as well as environmental parameters (temperature, conductivity, salinity, pH, dissolved oxygen, total organic carbon, total suspended solids, turbidity, total nitrogen, and total phosphorus). Water samples were collected from surface waters of urban catchments in Singapore. Salmonella and P. aeruginosa had significant positive correlations with most of the microbial indicators, especially E. coli and enterococci. Norovirus GII showed moderately strong positive correlations with most of the microbial indicators, except for HPyVs and coliphages. In general, high geometric means and significant correlations between human-specific markers and pathogens suggest the possibility of sewage contamination in some areas. The simultaneous detection of human-specific markers (i.e., B. thetaiotaomicron, M. smithii, and HPyVs) with E. coli and enterococcus supports the likelihood of recent fecal contamination, since the human-specific markers are unable to regrow in natural surface waters. Multiple-linear-regression results further confirm that the inclusion of M. smithii and HPyVs, together with traditional indicators, would better predict the occurrence of pathogens. Further study is needed to determine the applicability of such models to different geographical locations and environmental conditions.

Human astroviruses

Human astroviruses (HAtVs) are positive-sense single-stranded RNA viruses that were discovered in 1975. Astroviruses infecting other species, particularly mammalian and avian, were identified and classified into the genera Mamastrovirus and Avastrovirus. Through next-generation sequencing, many new astroviruses infecting different species, including humans, have been described, and the Astroviridae family shows a high diversity and zoonotic potential. Three divergent groups of HAstVs are recognized: the classic (MAstV 1), HAstV-MLB (MAstV 6), and HAstV-VA/HMO (MAstV 8 and MAstV 9) groups. Classic HAstVs contain 8 serotypes and account for 2 to 9% of all acute nonbacterial gastroenteritis in children worldwide. Infections are usually self-limiting but can also spread systemically and cause severe infections in immunocompromised patients. The other groups have also been identified in children with gastroenteritis, but extraintestinal pathologies have been suggested for them as well. Classic HAstVs may be grown in cells, allowing the study of their cell cycle, which is similar to that of caliciviruses. The continuous emergence of new astroviruses with a potential zoonotic transmission highlights the need to gain insights on their biology in order to prevent future health threats. This review focuses on the basic virology, pathogenesis, host response, epidemiology, diagnostic assays, and prevention strategies for HAstVs.

Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples

To secure food and water safety, quantitative information on multiple pathogens is important. In this study, we developed a microfluidic quantitative PCR (MFQPCR) system to simultaneously quantify 11 major human viral pathogens, including adenovirus, Aichi virus, astrovirus, enterovirus, human norovirus, rotavirus, sapovirus, and hepatitis A and E viruses. Murine norovirus and mengovirus were also quantified in our MFQPCR system as a sample processing control and an internal amplification control, respectively. River water contaminated with effluents from a wastewater treatment plant in Sapporo, Japan, was collected and used to validate our MFQPCR system for multiple viruses. High-throughput quantitative information was obtained with a quantification limit of 2 copies/μl of cDNA/DNA. Using this MFQPCR system, we could simultaneously quantify multiple viral pathogens in environmental water samples. The viral quantities obtained using MFQPCR were similar to those determined by conventional quantitative PCR. Thus, the MFQPCR system developed in this study can provide direct and quantitative information for viral pathogens, which is essential for risk assessments.

The application of new molecular methods in the investigation of a waterborne outbreak of norovirus in Denmark, 2012

In December 2012, an outbreak of acute gastrointestinal illness occurred in a geographical distinct area in Denmark covering 368 households. A combined microbiological, epidemiological and environmental investigation was initiated to understand the outbreak magnitude, pathogen(s) and vehicle in order to control the outbreak. Norovirus GII.4 New Orleans 2009 variant was detected in 15 of 17 individual stool samples from 14 households. Norovirus genomic material from water samples was detected and quantified and sequencing of longer parts of the viral capsid region (>1000 nt) were applied to patient and water samples. All five purposely selected water samples tested positive for norovirus GII in levels up to 1.8×10⁴ genomic units per 200 ml. Identical norovirus sequences were found in all 5 sequenced stool samples and 1 sequenced water sample, a second sequenced water sample showed 1 nt (<0.1%) difference. In a cohort study, including 256 participants, cases were defined as residents of the area experiencing diarrhoea or vomiting onset on 12–14 December 2012. We found an attack rate of 51%. Being a case was associated with drinking tap-water on 12–13 December (relative risk = 6.0, 95%CI: 1.6–22) and a dose-response relation for the mean glasses of tap-water consumed was observed. Environmental investigations suggested contamination from a sewage pipe to the drinking water due to fall in pressure during water supply system renovations. The combined microbiological, epidemiological and environmental investigations strongly indicates the outbreak was caused by norovirus contamination of the water supply system.